Longer stroke is a better "lever" for converting the pressure of combustion to rotational force at the crankshaft. The negative side is increased reciprocation forces, increased cylinder wall friction, and (as already mentioned) greater opportunities for heat loss to the cylinder walls.
It's basically the difference between torque and horsepower engines. The first gets its power at low speeds, while the second gets its power at high speeds.
There is another option not well understood by many and that is a modern derivative of the original aircraft rotary engine of WW1, a design that was long ago relegated to the scrap heap of history, but one that may have future applications, considering all of the modern advancements in metallurgy, fuel delivery, wireless communication, and lubrication.
regards
Mech
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